You need to elaborate what are you doing when not in Auto: Are you focusing manually (MF), single-shot (AF-C) or continuously (AF-C)? What apertures are you using? Shutter-speed? Still subjects? Moving? etc? Otherwise there are too many things that can go wrong!
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ItaiMar 3 '13 at 18:56

2 Answers
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Logic would say that if you are getting better results on auto, then why go manual? Manual is for those situations where auto won't cut it or is not appropriate.

To delve more into why you are getting poor results, we might need to know what it is you are actually doing, because saying "set the camera to auto" is ambiguous: you could mean you are switching the focusing from manual to auto focusing, or you could mean that you are changing the camera mode to the Full Auto mode.

Manual focusing:

This is relatively difficult on many modern DSLRs with ground-glass screens, or for that matter cameras with LCDs, though at least the latter might give you the option to have a zoomed-in preview while manual focusing.

The ground-glass screens on older DSLRs typically had a focusing guide in the centre of the screen which was basically a bunch of different angles cut into the glass, and the image had to line up on all the angled segments to indicate that it's in focus. It was a much more accurate way to manually focus than just looking directly at the ground glass image, which is soft due to the nature of ground glass anyway. Sadly the ground glass screens of low end modern DSLRs don't tend to have focus guides; they expect you will be automatically focusing.

If you do want to manually focus, you just need to work at it. Realise that a lot of the time what looks sharp on the ground glass won't be perfectly sharp, and you need to turn the focus back and forwards until you are in the "middle" of the "sharp" zone.

AF modes

Your camera will have multiple autofocus "zones", and it needs to know where in the picture you want it to attempt to focus.

You can set the camera to focus at a particular focus zone (centre or manual), or to automatically select all. This is your focus mode selection.

In the camera's full-auto mode, it usually will usually be set to the latter, so that people don't need to think about focusing (this is basically the case on all point-and-shoot cameras too). It will look at all of its autofocus zones and try to focus on whichever ones it thinks you most likely want. This will work a lot of the time, but fail sometimes.

If you set it to a manually-selected autofocus zone, or manually select one of the autofocus zones with the arrows, then it will ONLY look to focus in that one zone. You must be aiming the camera so that the subject you want to focus on is in that zone.

FWIW if the conditions are such that the autofocus can work, I find that it is almost always better than what I can do manually. Indeed, I watch the focus indicator in the viewfinder as much as the screen.

Remember too that the this series of nikons has a focus mode where it will shoot a frame whether it's focused or not. (The basis is that sometimes a blurry pic is better than no pic)

Finally: There is a corrective lens on the finder itself for adjusting for people who are near/far sighted. If this is set incorrectly, you will have a harder time judging the focus in the viewfinder.